infoseq

infoseq

infoseq is a small utility that lists the USA, name, accession number, type (nucleic or protein), length, percentage C+G, and/or description of a sequence.

Display information on a sequence:

% infoseq embl:paamir

Don't display the USA of a sequence:

% infoseq embl:paamir -nousa

Display only the name and length of a sequence:

% infoseq embl:paamir -only -name -length

Display only the description of a sequence:

% infoseq embl:paamir -only -desc

Display the type of a sequence:

% infoseq embl:paamir -only -type

Display information formatted with HTML:

% infoseq embl:paamir -html

Mandatory qualifiers:

[-sequence] (seqall)

Sequence database USA.

Optional qualifiers:

-outfile (outfile)

If you enter the name of a file here, this program will write the sequence details into that file.

-html (boolean)

Format output as an HTML table.

Advanced qualifiers:

-only (boolean)

This is a way of shortening the command line if you only want a few things to be displayed. Instead of specifying -nohead -noname -noacc -notype -nopgc -nodesc to get only the length output, you can specify -only -length.

-heading (boolean)

Display column headings.

-usa (boolean)

Display the USA of the sequence.

-name (boolean)

Display name column.

-accession (boolean)

Display accession column.

-gi (boolean)

Display GI column.

-version (boolean)

Display version column.

-type (boolean)

Display type column.

-length (boolean)

Display length column.

-pgc (boolean)

Display percent GC content column.

-description (boolean)

Display description column.



Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

Similar book on Amazon

flylib.com © 2008-2017.
If you may any questions please contact us: flylib@qtcs.net